drug-binding-site-definition
OfficialDefine a docking box from residues or a ligand.
Education & Research#virtual screening#molecular simulation#binding site#docking box#protein residues#ligand coordinates#JSON specification
Authorlearningmatter-mit
Version1.0.0
Installs0
System Documentation
What problem does it solve?
Define the exact docking/search box for a protein binding site so downstream docking and docking-box-dependent workflows operate in the correct coordinate frame.
Core Features & Use Cases
- Docking box generation in Angstroms: Computes standardized box center coordinates and box dimensions (size_x/size_y/size_z) that other drug-discovery skills can directly consume.
- Multiple input modes: Supports defining the box from a co-crystal ligand (recommended), from known binding-site residues, or by reloading a previously generated JSON specification.
- Practical validation hooks: Encourages sanity-checking pocket coverage and includes an optional visualization step to confirm the box overlays the intended pocket.
Quick Start
Use the skill to compute a docking box from your co-crystal ligand file by providing the ligand coordinates and choosing padding and minimum box size for Angstrom units.
Dependency Matrix
Required Modules
MDAnalysisnumpyrdkitpymol
Components
scripts
💻 Claude Code Installation
Recommended: Let Claude install automatically. Simply copy and paste the text below to Claude Code.
Please help me install this Skill: Name: drug-binding-site-definition Download link: https://github.com/learningmatter-mit/AtomisticSkills/archive/main.zip#drug-binding-site-definition Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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